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CGH Array Analysis Important
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Array Design
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CGH Array Analysis
CGH Array : The Reference DNA and the Test DNA were labeled with a fluorescent dye different each other, and were mixed.
By hybridizing the mixture to the slide where interested genes were spotted,
the fluorescence intensity of the Reference DNA and the Test DNA were compared.
By the above procedure, we can analyze deletion, and region of amplification in a target gene.
By changing design of probes, a comprehensive analysis of the whole genome is available.
And, by designing density probes for a specific region, detection of very small deletion or amplification in a genome DNA is available.
High Resolution, Improved Performance, Ultimate Confidence
We don't want to miss a small mutation ! We want to identify the breakpoint as accurately as possible !
In CGH analysis, the more narrow the probe interval, the more accurate detect the small mutation.
In 1x4.2M array, We can synthesize different kinds of 4,200,000 probe on one microarray slide.
By using the human catalog array for example, over the whole genome, it has been designed probes one by one
for every about 300bp, minimum CNV size can be detected about 1.5 kb achieve.
And, so the segment width is calculated by 300 bp, that excellent to identify the breakpoint.
High resolustion, Cost-Effective Solution
As the interesting domain has been identified, or the interesting domain in whole genome has been identified, a large number of samples in that will be needed. In the case, 12x135K multiplex custom array is effective for analysis.
Multiplex array, while allowing the analysis of high throughput, and the other, there are characterized by the number of probes available in each sub-array.
For Example , if you designed the very high density array, such as "each probe place one on each 100bp", It's possibility to analysis is about 13.5Mbp genome area (same as 1/3 size of Chromosome 21).
In this case, the minimul size of CNV detection is about 500 bp and high-resolution data can be obtained.
Burkitt's lymphoma

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Suspected chromosomal abnormality

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Induced pluripotent stem cells (iPS cells)

Campany data
Array Design
CGH Array analysis, the design of probe use Tiling-Array it designed regular intervals to get no-bias data for each region in the genome.
By some sequence not be able to design a probe, the intervals will not be exactly certain.
This is called the average probe interval that the average length of the 5'end position to 5'end oposition of next probe. (or calculated by Median) Measure of the length of the CNV can be detected is approximately 5 to 10 times of the probe interval.
Whole Genome CGH Array : The probe was designed for the whole genome without limiting the domain. For designed to analize the whole genome in a single array, resolution of the data depends on the array format.
* Human chromosome-specific array CGH(for each chromosome) is also usable in the case of analysis of human samples.
Schematic diagram for catalog array CGH analysis of whole human genome.
Focus Array : It is designed to detect mutations in the small domain by using a high density probes for the domain interested. On the other hand, by placing probes in some intervals on extent area of interested domain in the genome, backbone data can be obtained.
Array as a catalog of human exon focus array (in the region of human exon is able to design the probe always),
human CNV array (place the probe intensive region of human CNV),
CGX array (the probe is designed to focus on domain such as human disease-related) .
Schematic diagram for Human Focus Array : Exon Focus Array

Custom Array : In the case such as whole genome array, By designing in a multiplex array to place probe in high density at particular domain that was identified, Can be carried out at high cost performance and high-resolution high-throughput analysis.
Schematic array for high throughput analysis
What is CNV : CNV is that the copy number of genes that differ between individuals, a clear report was made as seen high-frequency polymorphism in the genome of a normal person, 2004
Understand that there is a possibility that the polymorphism is covering an domain of more than 10% of the human genome by the subsequent analysis, including disease susceptibility, and drug susceptibility,CNV is known as implicated widely in the human trait difference.
Key paper. Redon R, Ishikawa S, et al "Global variation in copy number in the human genome."
Nature. 2006 Nov 23;444(7118):444-54. PMID:9771718
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